Computational protocol: Population Genetic Analysis of Propionibacterium acnes Identifies a Subpopulation and Epidemic Clones Associated with Acne

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Protocol publication

[…] Phylogenetic and molecular evolutionary analyses were conducted using MEGA version 4.0 software . The Minimum evolution algorithm was applied based on the Nucleotide Maximum Composite Likelihood analysis of all positions. Bootstrap analysis was based on 500 replicates. For comparison, analyses were also conducted with the Neighbor Joining algorithm. For the recA, tly, and camp5 genes, sequences from previous studies deposited in public sequence databases were included in the analyses to allow reference to such studies. Estimates of genetic divergence at each gene locus were obtained in MEGA 4.0 and SplitsTree4 was used to compute unrooted phylogenetic networks from the concatenated sequences and for analysis of evidence of genetic recombination in the P.acnes population. The eBURSTv3 programme (http://eburst.mlst.net/default.asp) was used to identify clonal complexes and founders of such complexes according to Feil et al. . [...] The complete, annotated genome sequences of P. acnes strain KPA171202/DSM16379 (NC_006085) and strain SK137 (NC_014039) were compared. The origin of KPA171202/DSM16379 is referred to as “contamination of anaerobic culture” (Deutsche Sammlung von Mikroorganismen und Zellkulturen Catalogue) and SK137 as isolated from human skin. In addition, the non-closed genomes of strains SK187 (NZ_ADJM00000000), J165 (NZ_ADJL00000000), and J139 (NZ_ADFS00000000) were included in the analysis. The four latter genomes serve as reference for the Human Microbiome Project. The two complete genomes were aligned using MAUVE and ClustalX. To identify strain-specific gene pairs of orthologous genes, bidirectional BLASTp comparisons using the cut-off values ≥70% identity and ≥70% coverage. All protein sequences identified by this analysis were blasted against the remaining genomes. […]

Pipeline specifications

Software tools MEGA, SplitsTree, BURST, Mauve, Clustal W, BLASTP
Databases MLST.net ADFS HMP
Applications Phylogenetics, WGS analysis, Nucleotide sequence alignment
Organisms Cutibacterium acnes, Homo sapiens
Diseases Acne Vulgaris, Opportunistic Infections